Variant report

Variant	rs1039469
Chromosome Location	chr1:47487389-47487390
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr1:47487226-47487500	K562	blood:	n/a	n/a
2	REST	chr1:47487221-47487508	ECC-1	luminal epithelium:	n/a	n/a
3	REST	chr1:47487230-47487524	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr1:47486747-47487460	K562	blood:	n/a	n/a

Variant related genes	Relation type
CYP4X1	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1021827	0.81[EUR][1000 genomes]
rs1021828	0.81[EUR][1000 genomes]
rs1039468	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10890443	0.81[EUR][1000 genomes]
rs10890444	0.81[EUR][1000 genomes]
rs10890445	0.81[EUR][1000 genomes]
rs11211441	0.87[ASN][1000 genomes]
rs11211445	0.87[ASN][1000 genomes]
rs12030385	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12041262	0.87[AMR][1000 genomes]
rs12041324	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12045381	0.88[ASN][1000 genomes]
rs12140891	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12141009	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1502909	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1553390	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1827473	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1827474	0.81[EUR][1000 genomes]
rs1963620	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1986925	0.88[AMR][1000 genomes]
rs2036462	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2897114	0.88[AMR][1000 genomes]
rs4926728	0.85[ASN][1000 genomes]
rs4926776	0.86[ASN][1000 genomes]
rs55909645	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs66753730	0.88[AMR][1000 genomes]
rs72637973	0.83[ASN][1000 genomes]
rs9326151	0.81[EUR][1000 genomes]
rs9326152	0.81[EUR][1000 genomes]
rs9701888	0.88[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871958	chr1:47350374-47517123	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1009338	chr1:47358532-47555253	Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2763300	chr1:47358532-47628774	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv870695	chr1:47363893-47502714	Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv871288	chr1:47363893-47507808	Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv871377	chr1:47363893-47517123	Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv546166	chr1:47407739-47495605	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv870674	chr1:47416441-47517123	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv916813	chr1:47435635-47666179	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
10	nsv871717	chr1:47449486-47524264	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47484400-47489000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:47484800-47487600	Enhancers	Aorta	Aorta
3	chr1:47487000-47487400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:47487000-47487800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
5	chr1:47487200-47487800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:47487200-47487800	Enhancers	Adipose Nuclei	Adipose
7	chr1:47487200-47487800	Enhancers	Right Atrium	heart

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